Question: report error of methylkit
0
gravatar for ch8316f5eyu
2.4 years ago by
ch8316f5eyu0 wrote:
I cannot solve this error by myself. This is my code:
library(methylKit)
processBismarkAln(location = as.list(paste0(SRP010119_PATH, "Bismark/", SRP010119$Run, "_bismark_bt2.bamsort.bam")), 
                                             sample.id = as.list(SRP010119$Name), assembly = "mm10", save.folder =paste0(SRP010119_PATH, "methylKit") , save.context = c("CpG","CHG","CHH"), 
                                             read.context = "CpG", mincov = 5, treatment = SRP010119$Class)
myobjDB=methRead(as.list(paste0("/disk3/Data/RRBS/SRP010119_embryonic_development/methylKit/", SRP010119$Name, "_CpG.txt"))[1:3],
                                 sample.id=as.list(SRP010119$Name)[1:3],
                                 assembly="mm10",
                                 treatment=SRP010119$Class[1:3],
                                 context="CpG",
                                 dbtype = "tabix"
)
myobjDB=filterByCoverage(myobjDB,lo.count=5,lo.perc=NULL,
                                                                hi.count=NULL,hi.perc=99.9)
meth=unite(myobjDB, destrand=T, chunk.size = 1e7, mc.cores = 10)


The error I got is :

compressing the file with bgzip...
making tabix index...
compressing the file with bgzip...
making tabix index...
compressing the file with bgzip...
making tabix index...
[ti_index_core] the file out of order at line 176099
Error in value[[3L]](cond) : 
  internal: samtools invoked 'exit(1)'; see warnings() and restart R
  file: /home/zwy/methylDB 2017-07-06 O1P/oocytes_3_filtered_destrand.txt.bgz

Anyone know what is wrong?

 

methylkit • 658 views
ADD COMMENTlink modified 2.4 years ago by altuna akalin20 • written 2.4 years ago by ch8316f5eyu0

Hi,

I was wondering if ever overcame this error. It would be a lot of help.

Thanks,

ADD REPLYlink written 19 months ago by kalimero04110
Answer: report error of methylkit
0
gravatar for altuna akalin
2.4 years ago by
Germany/Berlin/MDC-BIMSB
altuna akalin20 wrote:
can you try dbtype = NA and see if the problems persists? Please also make sure you are using the latest version. If you want further assistance please send a reproducible example, https://stackoverflow.com/questions/5963269/how-to- make-a-great-r-reproducible-example On Wed, Jul 5, 2017 at 8:36 AM, <ewainblat@gmail.com> wrote: > Hello, > > I am currently trying to upload an output from BSMap and I receive the > error "*Error in `[.data.frame`(data, , coverage.col) : 5)) undefined > columns selected*" with the line > > obj=methRead("BSMap_file",sample.id="test",assembly="45", header=FALSE, > context="CpG", resolution="base",pipeline=list(fraction=TRUE, chr.col=1, > start.col=2,end.col=2,coverage.col=6,strand.col=3,freqC.col=5)). > > I made sure the coverage was an int with awk '{print $1, $2, > $3,$4,$5,int($6) }' BSMap_file > BSMap_file > > Thank you, > Ethan > > -- > You received this message because you are subscribed to the Google Groups > "methylkit_discussion" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to methylkit_discussion+unsubscribe@googlegroups.com. > To post to this group, send email to methylkit_discussion@googlegroups.com > . > Visit this group at https://groups.google.com/group/methylkit_discussion. > For more options, visit https://groups.google.com/d/optout. > On Thu, Jul 6, 2017 at 11:12 AM, ch8316f5eyu [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User ch8316f5eyu <https: support.bioconductor.org="" u="" 13405=""/> wrote Question: > report error of methylkit <https: support.bioconductor.org="" p="" 97823=""/>: > > I cannot solve this error by myself. This is my code: > > library(methylKit) > processBismarkAln(location = as.list(paste0(SRP010119_PATH, "Bismark/", SRP010119$Run, "_bismark_bt2.bamsort.bam")), > sample.id = as.list(SRP010119$Name), assembly = "mm10", save.folder =paste0(SRP010119_PATH, "methylKit") , save.context = c("CpG","CHG","CHH"), > read.context = "CpG", mincov = 5, treatment = SRP010119$Class) > myobjDB=methRead(as.list(paste0("/disk3/Data/RRBS/SRP010119_embryonic_development/methylKit/", SRP010119$Name, "_CpG.txt"))[1:3], > sample.id=as.list(SRP010119$Name)[1:3], > assembly="mm10", > treatment=SRP010119$Class[1:3], > context="CpG", > dbtype = "tabix" > ) > myobjDB=filterByCoverage(myobjDB,lo.count=5,lo.perc=NULL, > hi.count=NULL,hi.perc=99.9) > meth=unite(myobjDB, destrand=T, chunk.size = 1e7, mc.cores = 10) > > > The error I got is : > > compressing the file with bgzip... > making tabix index... > compressing the file with bgzip... > making tabix index... > compressing the file with bgzip... > making tabix index... > [ti_index_core] the file out of order at line 176099 > Error in value[[3L]](cond) : > internal: samtools invoked 'exit(1)'; see warnings() and restart R > file: /home/zwy/methylDB 2017-07-06 O1P/oocytes_3_filtered_destrand.txt.bgz > > Anyone know what is wrong? > > > > ------------------------------ > > Post tags: methylKit > > You may reply via email or visit report error of methylkit >
ADD COMMENTlink written 2.4 years ago by altuna akalin20
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